Contacts of the helix formed by residues 414 - 435 (chain B) in PDB entry 2XAR
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LYS 414 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ASP* 5.5 10.3 - - - +
65B GLU* 5.0 0.6 + - - -
322B TYR* 4.0 11.9 - - - +
412B PRO* 3.2 5.1 + - + +
413B LEU* 1.3 77.3 - - - +
415B ARG* 1.3 61.1 + - - +
416B MET 3.1 1.4 + - - -
417B GLU* 3.2 41.3 + - - +
418B SER* 4.2 0.7 + - - -
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Residues in contact with ARG 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ARG* 3.2 28.0 - - - +
48B ASP* 5.7 2.0 + - - -
411B LYS* 4.0 7.9 - - - +
412B PRO* 3.0 46.6 + - + +
413B LEU 3.0 0.6 + - - -
414B LYS* 1.3 73.2 - - - +
416B MET* 1.3 55.3 + - - +
417B GLU 3.0 2.5 - - - -
418B SER* 2.9 26.2 + - - +
419B TYR* 2.7 57.0 + - + -
500B IHP 2.9 59.3 + - - -
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Residues in contact with MET 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B ILE* 3.6 26.9 - - + +
318B ALA* 4.0 32.3 - - + +
319B ILE* 3.4 15.0 - - - +
322B TYR* 3.5 33.2 - - + -
357B VAL* 4.3 10.8 - - + -
360B TYR* 3.4 31.6 - - + -
361B LEU* 3.9 16.6 - - + +
412B PRO 4.4 0.2 + - - -
413B LEU* 3.1 23.3 + - + +
415B ARG* 1.3 76.6 - - - +
417B GLU* 1.3 59.3 + - - +
419B TYR* 3.6 7.4 + - - +
420B TYR 3.4 14.9 + - - -
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Residues in contact with GLU 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B ILE* 4.4 5.2 - - - -
322B TYR* 3.2 38.9 + - + +
323B TYR* 3.8 22.4 + - - +
326B ILE* 5.1 2.4 - - - +
328B GLN* 5.3 2.3 + - - +
414B LYS* 3.2 29.7 + - - +
415B ARG 3.0 0.4 - - - -
416B MET* 1.3 75.7 - - - +
418B SER* 1.3 64.5 + - - +
420B TYR* 3.3 6.2 + - - +
421B LYS* 3.2 37.6 + - - +
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Residues in contact with SER 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B LYS 4.2 1.0 + - - -
415B ARG* 2.9 32.0 + - - +
417B GLU* 1.3 77.6 - - - +
419B TYR* 1.3 59.0 + - - +
421B LYS* 3.9 8.8 - - - +
422B LEU* 2.9 32.5 + - - +
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Residues in contact with TYR 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B ARG* 4.7 9.0 + - - +
315B ILE* 3.9 12.9 - - + +
360B TYR* 3.7 33.2 - + - +
361B LEU* 4.3 13.9 - - + -
364B ALA* 4.0 8.8 - - + +
411B LYS* 3.5 19.1 - - - +
415B ARG* 2.7 51.8 + - + +
416B MET* 3.7 10.5 - - - +
418B SER* 1.3 74.4 + - - +
420B TYR* 1.3 57.1 + - - +
422B LEU* 3.6 10.5 - - + +
423B ASP* 3.0 30.1 + - - +
500B IHP 2.5 48.9 + - - -
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Residues in contact with TYR 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B ILE* 3.5 22.3 - - + +
316B GLU* 4.3 24.5 + - + +
319B ILE* 3.7 39.7 - - + -
332B ILE* 3.5 43.9 - - + +
416B MET 3.4 7.6 + - - +
417B GLU 3.3 9.2 + - - +
419B TYR* 1.3 76.2 - - - +
421B LYS* 1.3 75.0 + - + +
422B LEU 3.3 0.2 + - - -
423B ASP* 3.4 2.3 + - - +
424B LYS* 2.9 52.8 + - + +
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Residues in contact with LYS 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417B GLU* 3.2 26.5 + - - +
418B SER* 3.9 7.6 - - - +
420B TYR* 1.3 88.0 - - + +
422B LEU* 1.3 58.1 + - - +
424B LYS* 3.6 8.1 - - + +
425B LYS* 3.0 30.5 + - - +
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Residues in contact with LEU 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B ARG* 3.9 20.9 - - - +
196B HIS* 3.9 22.9 - - - +
199B LEU* 4.8 7.4 - - + -
418B SER 2.9 19.3 + - - +
419B TYR* 3.6 9.9 - - + +
421B LYS* 1.3 76.0 - - - +
423B ASP* 1.3 57.7 + - - +
425B LYS* 3.0 15.4 + - + +
426B ILE* 2.9 41.5 + - + +
500B IHP 3.9 19.7 - - - +
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Residues in contact with ASP 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B LYS* 2.6 43.2 + - - +
192B ARG* 2.7 34.6 + - - +
195B MET* 5.6 2.3 - - - +
314B ASP* 5.3 1.7 - - - +
315B ILE* 3.4 22.5 - - + +
316B GLU* 4.2 4.9 - - - +
419B TYR 3.0 17.8 + - - +
420B TYR* 3.8 1.7 - - - +
422B LEU* 1.3 75.2 - - - +
424B LYS* 1.3 65.8 + - - +
426B ILE* 3.0 16.8 + - - +
427B ILE* 3.0 14.8 + - - +
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Residues in contact with LYS 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B ASN* 5.8 4.0 - - - +
316B GLU* 5.8 2.0 - - - +
332B ILE* 6.3 0.2 - - - +
420B TYR* 2.9 46.1 + - + +
421B LYS* 3.6 7.2 - - + +
423B ASP* 1.3 76.0 + - - +
425B LYS* 1.3 52.3 + - - +
427B ILE* 3.3 12.6 - - + +
428B SER* 2.6 42.2 + - - +
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Residues in contact with LYS 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B LEU* 3.9 20.3 - - + +
203B TYR* 3.2 46.5 + - - -
421B LYS 3.0 15.7 + - - +
422B LEU* 3.1 21.2 - - + +
424B LYS* 1.3 74.7 - - - +
426B ILE* 1.3 62.4 + - - +
428B SER* 3.0 15.4 + - - -
429B PHE* 3.1 17.2 + - + +
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Residues in contact with ILE 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B ARG* 4.7 9.2 - - - +
195B MET* 3.5 46.8 - - + +
196B HIS* 3.1 39.9 - - + +
199B LEU* 3.2 31.6 - - + -
422B LEU* 2.9 30.5 + - + +
423B ASP* 3.0 11.9 + - - +
425B LYS* 1.3 76.4 - - - +
427B ILE* 1.3 59.4 + - + +
429B PHE* 3.3 4.7 + - - +
430B TYR* 2.9 27.9 + - - +
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Residues in contact with ILE 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B ASN* 3.7 35.7 - - + +
186B LEU* 4.3 9.0 - - + -
187B LYS* 3.8 29.4 - - + -
195B MET* 3.7 27.4 - - + -
423B ASP* 3.0 18.7 + - - +
424B LYS* 3.3 22.0 - - + +
426B ILE* 1.3 76.2 - - + +
428B SER* 1.3 59.8 + - - +
430B TYR* 4.4 3.8 - - + -
431B ASN* 3.0 55.4 + - - +
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Residues in contact with SER 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B ASN* 5.8 0.4 - - - -
424B LYS* 2.6 29.9 + - - +
425B LYS* 3.0 14.7 + - - -
427B ILE* 1.3 75.3 - - - +
429B PHE* 1.3 57.4 + - - +
431B ASN* 3.4 8.4 + - - +
432B ARG* 2.8 31.6 + - - +
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Residues in contact with PHE 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195B MET 5.6 0.9 - - - -
198B LEU* 3.2 42.2 - - + -
199B LEU* 3.8 23.1 - - + -
202B GLU* 3.3 44.6 - - + -
203B TYR* 6.0 0.4 - + - -
425B LYS* 3.1 18.4 + - + +
426B ILE 3.8 3.1 - - - +
428B SER* 1.3 78.0 + - - +
430B TYR* 1.3 62.8 + - - +
432B ARG* 3.5 23.3 - - - +
433B LYS* 3.1 49.9 + - + +
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Residues in contact with TYR 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B LEU* 4.2 22.2 - - + -
190B VAL* 4.1 29.3 - - + +
194B LYS* 4.5 17.5 + - + -
195B MET* 3.8 45.8 - - + +
198B LEU* 3.4 33.6 - - + +
426B ILE 2.9 17.0 + - - +
427B ILE* 4.0 4.7 - - + +
428B SER 3.3 0.4 - - - -
429B PHE* 1.3 78.6 - - - +
431B ASN* 1.3 65.8 + - - +
433B LYS* 3.4 2.1 + - - +
434B GLN* 3.1 58.4 + - - +
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Residues in contact with ASN 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B GLU* 3.2 31.8 + - - +
184B ASN* 4.1 4.2 + - - -
186B LEU* 3.5 27.9 - - - +
427B ILE* 3.0 35.2 + - - +
428B SER* 3.7 7.3 - - - +
430B TYR* 1.3 74.8 - - - +
432B ARG* 1.3 64.5 + - - +
434B GLN* 3.2 10.5 + - - +
435B LYS* 3.5 31.1 + - - +
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Residues in contact with ARG 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428B SER 2.8 18.6 + - - +
429B PHE* 3.5 26.4 - - + +
431B ASN* 1.3 78.2 - - - +
433B LYS* 1.3 61.8 + - + +
434B GLN 3.6 0.5 + - - -
435B LYS* 4.1 8.0 + - - +
436B ALA* 4.4 4.7 + - - +
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Residues in contact with LYS 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B LEU* 3.4 36.6 - - + +
201B LEU* 5.9 1.0 - - - +
202B GLU* 4.9 6.2 + - - +
429B PHE* 3.1 46.8 + - + +
430B TYR 3.8 2.0 - - - +
431B ASN 3.3 0.2 - - - -
432B ARG* 1.3 75.7 - - + +
434B GLN* 1.3 63.9 + - - +
435B LYS 3.3 3.1 - - - -
436B ALA* 3.5 26.0 - - + +
437B GLU* 3.4 9.5 - - - +
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Residues in contact with GLN 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B LEU* 4.6 10.1 - - + -
198B LEU* 5.1 3.8 - - - +
430B TYR* 3.1 52.7 + - + +
431B ASN* 3.2 9.2 + - - +
433B LYS* 1.3 77.5 - - - +
435B LYS* 1.3 70.8 + - + +
436B ALA 3.4 0.2 - - - -
437B GLU* 2.9 31.2 + - - +
438B ASN* 3.3 19.7 + - - +
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Residues in contact with LYS 435 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B LEU* 4.6 8.5 - - - +
431B ASN* 3.5 35.0 + - - +
432B ARG 4.1 4.8 + - - +
433B LYS 3.3 0.2 - - - -
434B GLN* 1.3 90.2 - - - +
436B ALA* 1.3 58.4 + - - +
437B GLU 3.1 6.8 + - - -
438B ASN* 3.8 34.5 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il